Maybe the attached files will give you an idea. t33.pl is the program file, fasta_dat.txt is the data file and junk.txt is the output from the program.

I used a smaller window size because my sample fasta file sequences weren't as long as the ones you have and the skip is smaller too. You would just need to make those adjustments for your program.

Look it over and ask any questions.

Hope this helps.

Update: Made a change to t33.pl

if ($begin_pos + $window_size > $length)

to

if ($begin_pos + $window_size >= $length)

Update2: Just to show a possible output ordered by skew, (uses SQLite database, pretty simple). File is bio_stat_db.pl.

Update3: Made adjustments to t33.pl and bio_stat_db.pl. Changed from $window_size to $size_read for skew calculations. Laurent caught this error (later in this thread). Output is now at the end of the 2 program files (after the __END__ token).